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In Print: Last Week's Microarray Papers of Note: Sep 24, 2013


IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds.

Invest Ophthalmol Vis Sci. 2013 Sep 17. [Epub ahead of print]

Goldstein O, et al.

The authors used Illumina and Affymetrix canine SNP genotyping arrays to identify the causative mutations in two early onset canine retinal degenerations, segregating in the American Staffordshire terrier and the Pitt bull terrier breeds.

The evaluation of the usefulness of pedigree verification-dedicated SNPs for breed assignment in three polish cattle populations.

Mol Biol Rep. 2013 Sep 22. [Epub ahead of print]

Gurgul A, et al.

In this study, the authors attempted to determine the breed of origin of 741 cattle by using 120 SNPs dedicated for parentage testing and included in Illumina's BovineSNP50 BeadChip genotyping assay. While the applied Bayesian and frequency-based methods allowed such differentiation, they report that the reliability of the results was "not completely satisfying," and suggest that the studied markers are "not the best tool for breed assignment."

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.

Bioinformatics. 2013 Sep 20. [Epub ahead of print]

Tarca A, et al.

The authors describe the results of an international collaboration called the IMPROVER Diagnostic Signature Challenge. Fifty-four teams used public data to develop prediction models in four disease areas including multiple sclerosis, lung cancer, psoriasis and chronic obstructive pulmonary disease, and made predictions on blinded new data that was generated. This paper presents the challenge results and introduces to the community the approaches of the best overall three performers, as well as an R package that implements the approach of the best team.

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.